{ "cells": [ { "cell_type": "markdown", "id": "939102b0-2779-4dbd-adfd-64eb06c39a13", "metadata": {}, "source": [ "# ST-Gears\n", "\n", "ST-Gears is a strong 3D reconstruction tool for Spatial Transcriptomics, with accurate position alignment plus distortion correction [[Xia23](https://www.biorxiv.org/content/10.1101/2023.12.09.570320v1)].\n", "\n", "ST-Gears consists of methods to compute anchors, to align rigidly and to registrate sections elastically:\n", "\n", "1. `st_gears` the main method which computes mappings between adjacent sections in serial, using Fused-Gromov Wasserstein Optimal Transport with our innovatie Distributive Constraints.\n", " \n", "2. `stack_slices_pairwise_rigid` rigidly aligns sections using Procrustes Analysis.\n", " \n", "3. `stack_slices_pairwise_elas_field` eliminates distorsions through Gaussian Smoothed Elastic Fields. Validity is proved mathematically." ] }, { "cell_type": "markdown", "id": "efe84931", "metadata": {}, "source": [ "This function can be run on GPU, if you want to use GPU, you need to create an environment according to the guide [Clustering_by_GPU](../Tutorials/Clustering_by_GPU.html).\n", "\n", "\n", "